An improved germline genome assembly for the sea lamprey Petromyzon marinus illuminates the evolution of germline-specific chromosomes.
An improved germline genome assembly for the sea lamprey Petromyzon marinus illuminates the evolution of germline-specific chromosomes.
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DOI：
10.1016/j.celrep.2023.112263
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发表时间：
2023-03-28
期刊：
影响因子：
8.8
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中科院分区：
文献类型：
--
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程序性DNA丢失是一种基因沉默机制，适用于几种脊椎动物和非脊椎动物谱系，包括所有现存的无颌脊椎动物和鸣禽。重建这些物种的体细胞消除（种系特异性）序列的进化已被证明是具有挑战性的，因为在消除的序列中重复和基因重复的含量很高，并且相应缺乏这些区域的高度精确和连续的组装。在这里，我们提出了一种改进的海七鳃鳗（Petromyzon marinus）基因组组装，该基因组组装是使用最近标准化的方法生成的，该方法增加了脊椎动物基因组组装的连续性和准确性。这种组装分解了高度连续的、保留的染色体和至少一条生殖系特异性染色体，从而允许进行新的分析，重建基因募集到生殖系特异性部分的时间、模式和影响。这些分析揭示了染色体间复制、染色体内复制和生殖系功能的正选择在生殖系特异性染色体的长期进化中所起的主要作用。Timoshevskaya等人报道了一种改进的海七鳃鳗基因组组装方法，该方法有助于解决在发育过程中被程序性消除的染色体（种系特异性染色体）的结构和进化。利用其他物种的数据，这些分析表明了复制和选择在生殖系特异性染色体的长期进化中的主要作用。
Programmed DNA loss is a gene silencing mechanism that is employed by several vertebrate and nonvertebrate lineages, including all living jawless vertebrates and songbirds. Reconstructing the evolution of somatically eliminated (germline-specific) sequences in these species has proven challenging due to a high content of repeats and gene duplications in eliminated sequences and a corresponding lack of highly accurate and contiguous assemblies for these regions. Here, we present an improved assembly of the sea lamprey (Petromyzon marinus) genome that was generated using recently standardized methods that increase the contiguity and accuracy of vertebrate genome assemblies. This assembly resolves highly contiguous, somatically retained chromosomes and at least one germline-specific chromosome, permitting new analyses that reconstruct the timing, mode, and repercussions of recruitment of genes to the germline-specific fraction. These analyses reveal major roles of interchromosomal segmental duplication, intrachromosomal duplication, and positive selection for germline functions in the long-term evolution of germline-specific chromosomes. Timoshevskaya et al. report an improved genome assembly for sea lamprey that aids in resolving the structure and evolution of chromosomes that are programmatically eliminated during development (germline-specific chromosomes). Using data from other species, these analyses indicate major roles of duplication and selection in the long-term evolution of germline-specific chromosomes.
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